Locus 1207

Sequence ID X_DroMel_CAF1
Location 3,588,185 – 3,588,292
Length 107
Max. P 0.794487
window1941 window1942

overview

Window 1

Location 3,588,185 – 3,588,292
Length 107
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 85.56
Mean single sequence MFE -17.70
Consensus MFE -14.68
Energy contribution -14.68
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.83
SVM decision value 0.60
SVM RNA-class probability 0.794487
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3588185 107 + 22224390
CGCACUCACCUUCACCACACACAAAAACAUCUCUAUAUCCCCGUAUAAUGUGGUGUAUGUUUAUAUACAAUAGGGGAUAUACGUUUGUAAACCUCACCACAC--------ACACG
..........................(((....(((((((((.(((..((((.((((....))))))))))))))))))))....)))..............--------..... ( -17.90)
>DroSec_CAF1 47158 107 + 1
CGCACUCACCUUCACCACACACAAAAACAUCUCUAUAUCAACGUAUAAUGUGGUGUAUGUUUAUAUACAAUAGGGGAUAUACGUUUGUAAACCUCACCACAC--------ACACG
.........................................(((....(((((((...(((((((.((.(((.....)))..)).)))))))..))))))).--------..))) ( -16.70)
>DroEre_CAF1 42038 112 + 1
CGCACUCACCUUCACCACACACAAAAACAUCUCUAUAUUGCUGUAGAAUGUGGUGUAUGUUUAUAU---AUAGGGGAUAUACGAUUGUAAACCCCACCACACACACACACACACA
...............................((((((....)))))).((((((((((((....))---)))(((..((((....))))..)))))))))).............. ( -20.20)
>DroYak_CAF1 42926 97 + 1
CGCACUCACCUUCACCACACACAAAAACAU---------AAUGUAUAAUGUGGUGUAUGUUUAUAUAU-AUAUGGUAUAUACGUUUGUAAACCUCACCACAC--------ACACG
..............................---------.........(((((((...(((((((.(.-.((((...))))..).)))))))..))))))).--------..... ( -16.00)
>consensus
CGCACUCACCUUCACCACACACAAAAACAUCUCUAUAUCAACGUAUAAUGUGGUGUAUGUUUAUAUAC_AUAGGGGAUAUACGUUUGUAAACCUCACCACAC________ACACG
................................................(((((((...(((((((....(((.....))).....)))))))..))))))).............. (-14.68 = -14.68 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,588,185 – 3,588,292
Length 107
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 85.56
Mean single sequence MFE -30.87
Consensus MFE -17.96
Energy contribution -18.90
Covariance contribution 0.94
Combinations/Pair 1.09
Mean z-score -2.49
Structure conservation index 0.58
SVM decision value 0.20
SVM RNA-class probability 0.630768
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3588185 107 - 22224390
CGUGU--------GUGUGGUGAGGUUUACAAACGUAUAUCCCCUAUUGUAUAUAAACAUACACCACAUUAUACGGGGAUAUAGAGAUGUUUUUGUGUGUGGUGAAGGUGAGUGCG
..(((--------(((..(((.((..(((....)))....)).)))..))))))..(((.((((((((...((((((((((....))))))))))))))))))...)))...... ( -28.70)
>DroSec_CAF1 47158 107 - 1
CGUGU--------GUGUGGUGAGGUUUACAAACGUAUAUCCCCUAUUGUAUAUAAACAUACACCACAUUAUACGUUGAUAUAGAGAUGUUUUUGUGUGUGGUGAAGGUGAGUGCG
..(((--------(((..(((.((..(((....)))....)).)))..))))))..(((.((((((((...(((..(((((....)))))..)))))))))))...)))...... ( -26.40)
>DroEre_CAF1 42038 112 - 1
UGUGUGUGUGUGUGUGUGGUGGGGUUUACAAUCGUAUAUCCCCUAU---AUAUAAACAUACACCACAUUCUACAGCAAUAUAGAGAUGUUUUUGUGUGUGGUGAAGGUGAGUGCG
.((((((((.(((((((((.(((((.(((....))).)))))))))---))))).))))))))(((.(((.((.(((.(((((((....)))))))))).))))).)))...... ( -39.60)
>DroYak_CAF1 42926 97 - 1
CGUGU--------GUGUGGUGAGGUUUACAAACGUAUAUACCAUAU-AUAUAUAAACAUACACCACAUUAUACAUU---------AUGUUUUUGUGUGUGGUGAAGGUGAGUGCG
.((((--------((((((((.....(((....)))..))))))))-)))).....(((.((((.((((((((((.---------........))))))))))..)))).))).. ( -28.80)
>consensus
CGUGU________GUGUGGUGAGGUUUACAAACGUAUAUCCCCUAU_GUAUAUAAACAUACACCACAUUAUACAGUGAUAUAGAGAUGUUUUUGUGUGUGGUGAAGGUGAGUGCG
((..(........(((..(((.((..(((....)))....)).)))..))).....(((.((((((((...(((..(((((....)))))..)))))))))))...))).)..)) (-17.96 = -18.90 +   0.94)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:57 2006